Index

_

__init__() built-in function __init__() (bmiptools.core.base.CoreBasic method) (bmiptools.core.utils.ExifreadEncoder method) (bmiptools.core.utils.NumpyEncoder method) (bmiptools.gui.bmiptools_gui.BMIPToolsGUI method) (bmiptools.gui.bmiptools_gui.PipelineBuilder method) (bmiptools.gui.bmiptools_gui.PipelineLoad method) (bmiptools.gui.bmiptools_gui.PipelineTemplateLoad method) (bmiptools.gui.bmiptools_gui.PreviewSetting method) (bmiptools.gui.bmiptools_gui.StackSave method) (bmiptools.gui.gui_basic.GuiPI method) (bmiptools.gui.gui_basic.GuizeObject method) (bmiptools.gui.gui_basic.GuizeObjectFromDict method) (bmiptools.pipeline.Pipeline method) (bmiptools.stack.ExperimentalMetadataInspector method) (bmiptools.stack.Stack method) (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.geometric.geometric_tools.RodriguesVector method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method) (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic2D method) (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic3D method)

_setup()

A

add_metadata() (bmiptools.stack.Stack method)

Affine (class in bmiptools.transformation.geometric.affine) apply() (bmiptools.pipeline.Pipeline method)

B

Basic2D (class in bmiptools.visualization.graphic_tools.basic_graphic_tools) Basic3D (class in bmiptools.visualization.graphic_tools.basic_graphic_tools) bmiptools.core.base module bmiptools.core.gpu_utils module bmiptools.core.ip_utils module bmiptools.core.math_utils module bmiptools.core.utils module bmiptools.gui.bmiptools_gui module bmiptools.gui.gui_basic module bmiptools.pipeline module bmiptools.setting.configure module bmiptools.setting.installed_plugins module bmiptools.stack module bmiptools.transformation.alignment.registrator module bmiptools.transformation.base module bmiptools.transformation.basic.filters module

bmiptools.transformation.dynamics.equalizer module bmiptools.transformation.dynamics.histogram_matcher module bmiptools.transformation.dynamics.standardizer module bmiptools.transformation.geometric.affine module bmiptools.transformation.geometric.cropper module bmiptools.transformation.geometric.geometric_tools module bmiptools.transformation.restoration._restoration_shared module bmiptools.transformation.restoration.decharger module bmiptools.transformation.restoration.denoiser module bmiptools.transformation.restoration.destriper module bmiptools.transformation.restoration.flatter module bmiptools.visualization.geometric.change_coordinate_system module bmiptools.visualization.graphic_tools.basic_graphic_tools module BMIPToolsGUI (class in bmiptools.gui.bmiptools_gui) built-in function __init__() widget()

C

cartesian_to_cylindircal() (in module bmiptools.core.math_utils) cartesian_to_spherical() (in module bmiptools.core.math_utils) ChangeCoordinateSystem (class in bmiptools.visualization.geometric.change_coordinate_system) clean_line() (bmiptools.stack.ExperimentalMetadataInspector static method) compare_images() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic2D static method)

copy_folder_and_its_content() (in module bmiptools.core.utils) CoreBasic (class in bmiptools.core.base) create() (bmiptools.pipeline.Pipeline method) Cropper (class in bmiptools.transformation.geometric.cropper) cylindrical_to_cartesian() (in module bmiptools.core.math_utils)

D

Decharger (class in bmiptools.transformation.restoration.decharger) default() (bmiptools.core.utils.ExifreadEncoder method) (bmiptools.core.utils.NumpyEncoder method)

delete_folder_and_its_content() (in module bmiptools.core.utils) Denoiser (class in bmiptools.transformation.restoration.denoiser) DenoiserDNN (class in bmiptools.transformation.restoration.denoiser) Destriper (class in bmiptools.transformation.restoration.destriper)

E

encode() (bmiptools.core.utils.ExifreadEncoder method) (bmiptools.core.utils.NumpyEncoder method)

Equalizer (class in bmiptools.transformation.dynamics.equalizer) ExifreadEncoder (class in bmiptools.core.utils) ExperimentalMetadataInspector (class in bmiptools.stack)

F

fit() (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

Flatter (class in bmiptools.transformation.restoration.flatter) FloatRangeText() (in module bmiptools.gui.gui_basic) FloatRangeText_get_value() (in module bmiptools.gui.gui_basic) FloatRangeText_set_value() (in module bmiptools.gui.gui_basic) FloatSpace() (in module bmiptools.gui.gui_basic) FloatSpace_get_value() (in module bmiptools.gui.gui_basic) FloatSpace_set_value() (in module bmiptools.gui.gui_basic) FloatSpaceText() (in module bmiptools.gui.gui_basic) FloatSpaceText_get_value() (in module bmiptools.gui.gui_basic) FloatSpaceText_set_value() (in module bmiptools.gui.gui_basic) from_array() (bmiptools.stack.Stack method)

G

gaussian_filter2d() (in module bmiptools.transformation.basic.filters) gaussian_filterNd() (in module bmiptools.transformation.basic.filters) generate_parameter_space() (in module bmiptools.transformation.restoration._restoration_shared) get_branch_of_key_tree() (in module bmiptools.core.utils) get_by_path() (in module bmiptools.core.utils) get_dimension_in_RAM() (bmiptools.stack.Stack method) get_transformation_dictionary() (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

grad_to_rad() (in module bmiptools.core.math_utils) GuiPI (class in bmiptools.gui.gui_basic) guize() (in module bmiptools.gui.gui_basic) GuizeObject (class in bmiptools.gui.gui_basic) GuizeObjectFromDict (class in bmiptools.gui.gui_basic)

H

HistogramMatcher (class in bmiptools.transformation.dynamics.histogram_matcher)

I

initialize() (bmiptools.pipeline.Pipeline method) install_plugin() (in module bmiptools.setting.configure) IntSpace() (in module bmiptools.gui.gui_basic) IntSpace_get_value() (in module bmiptools.gui.gui_basic) IntSpace_set_value() (in module bmiptools.gui.gui_basic) inverse_transform() (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

is_diagonal() (in module bmiptools.core.math_utils) is_even() (in module bmiptools.core.math_utils) isfloat() (in module bmiptools.core.utils) isnumeric() (bmiptools.stack.ExperimentalMetadataInspector static method) iterencode() (bmiptools.core.utils.ExifreadEncoder method) (bmiptools.core.utils.NumpyEncoder method)

K

kill_line() (in module bmiptools.core.ip_utils)

L

list_to_string() (in module bmiptools.core.utils) load() (bmiptools.pipeline.Pipeline method) load_pipeline_template_from_json() (bmiptools.pipeline.Pipeline method) load_recognized_metadata_tag_list() (bmiptools.stack.ExperimentalMetadataInspector method)

load_registration() (bmiptools.transformation.alignment.registrator.Registrator method) load_slices() (bmiptools.stack.Stack method) load_slices_from_folder() (bmiptools.stack.Stack method) load_stack() (bmiptools.stack.Stack method) load_stack_from_folder() (bmiptools.stack.Stack method)

M

manage_path() (in module bmiptools.core.utils) max_and_min() (in module bmiptools.core.math_utils) module bmiptools.core.base bmiptools.core.gpu_utils bmiptools.core.ip_utils bmiptools.core.math_utils bmiptools.core.utils bmiptools.gui.bmiptools_gui bmiptools.gui.gui_basic bmiptools.pipeline bmiptools.setting.configure bmiptools.setting.installed_plugins bmiptools.stack bmiptools.transformation.alignment.registrator bmiptools.transformation.base bmiptools.transformation.basic.filters bmiptools.transformation.dynamics.equalizer bmiptools.transformation.dynamics.histogram_matcher bmiptools.transformation.dynamics.standardizer bmiptools.transformation.geometric.affine bmiptools.transformation.geometric.cropper bmiptools.transformation.geometric.geometric_tools bmiptools.transformation.restoration._restoration_shared bmiptools.transformation.restoration.decharger bmiptools.transformation.restoration.denoiser bmiptools.transformation.restoration.destriper bmiptools.transformation.restoration.flatter bmiptools.visualization.geometric.change_coordinate_system bmiptools.visualization.graphic_tools.basic_graphic_tools

N

NumpyEncoder (class in bmiptools.core.utils)

P

Pipeline (class in bmiptools.pipeline) PipelineBuilder (class in bmiptools.gui.bmiptools_gui) PipelineLoad (class in bmiptools.gui.bmiptools_gui) PipelineTemplateLoad (class in bmiptools.gui.bmiptools_gui) plot_3d_binary_mask() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic3D static method) plot_3d_points() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic3D static method) plot_image_as_surface() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic2D static method) PreviewSetting (class in bmiptools.gui.bmiptools_gui) progress_bar() (bmiptools.core.base.CoreBasic method) (bmiptools.pipeline.Pipeline method) (bmiptools.stack.Stack method) (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

R

rad_to_grad() (in module bmiptools.core.math_utils) read_global_setting() (in module bmiptools.core.utils)

read_metadata() (bmiptools.stack.ExperimentalMetadataInspector method) Registrator (class in bmiptools.transformation.alignment.registrator) RodriguesVector (class in bmiptools.transformation.geometric.geometric_tools)

S

save() (bmiptools.pipeline.Pipeline method) (bmiptools.stack.Stack method) (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method) save_as_gif() (bmiptools.stack.Stack method) save_registration() (bmiptools.transformation.alignment.registrator.Registrator method) set_by_path() (in module bmiptools.core.utils)

set_cpu_buffer() (in module bmiptools.setting.configure) set_in_a_nested_dict() (in module bmiptools.core.utils) set_multiprocessing_type() (in module bmiptools.setting.configure) set_option_in_global_setting() (in module bmiptools.core.utils) set_use_gpu() (in module bmiptools.setting.configure) set_use_multiprocessing() (in module bmiptools.setting.configure) set_verbosity() (in module bmiptools.setting.configure) setup_preview() (bmiptools.pipeline.Pipeline method) show_image() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic2D static method) show_stack() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic3D static method) show_threshold_on_image() (bmiptools.visualization.graphic_tools.basic_graphic_tools.Basic2D static method) smoothed_deriv() (in module bmiptools.core.ip_utils) spherical_to_cartesian() (in module bmiptools.core.math_utils) Stack (class in bmiptools.stack) StackSave (class in bmiptools.gui.bmiptools_gui) standard_number() (in module bmiptools.core.utils) Standardizer (class in bmiptools.transformation.dynamics.standardizer) standardizer() (in module bmiptools.core.ip_utils) statistics() (bmiptools.stack.Stack method)

T

transform() (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

TransformationBasic (class in bmiptools.transformation.base)

U

uninstall_plugin() (in module bmiptools.setting.configure)

V

vtqdm() (bmiptools.core.base.CoreBasic method) (bmiptools.pipeline.Pipeline method) (bmiptools.stack.Stack method) (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method)

W

widget() built-in function widget() (bmiptools.gui.gui_basic.GuiPI method) write() (bmiptools.core.base.CoreBasic method) (bmiptools.pipeline.Pipeline method) (bmiptools.stack.Stack method) (bmiptools.transformation.alignment.registrator.Registrator method) (bmiptools.transformation.base.TransformationBasic method) (bmiptools.transformation.dynamics.equalizer.Equalizer method) (bmiptools.transformation.dynamics.histogram_matcher.HistogramMatcher method) (bmiptools.transformation.dynamics.standardizer.Standardizer method) (bmiptools.transformation.geometric.affine.Affine method) (bmiptools.transformation.geometric.cropper.Cropper method) (bmiptools.transformation.restoration.decharger.Decharger method) (bmiptools.transformation.restoration.denoiser.Denoiser method) (bmiptools.transformation.restoration.denoiser.DenoiserDNN method) (bmiptools.transformation.restoration.destriper.Destriper method) (bmiptools.transformation.restoration.flatter.Flatter method) (bmiptools.visualization.geometric.change_coordinate_system.ChangeCoordinateSystem method) (in module bmiptools.core.utils)